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1. Getting Started
Before installing DEN-IM, a few dependencies must be installed in your system.
Nextflow (version 0.31.0 or higher) can be used on any POSIX compatible system (Linux, OS X, etc). It requires BASH and Java 8 (or higher) to be installed. You can confirm what version of java you have installed with
java -version
Note: When running Nextflow with Java 9 a few warnings will be emitted as it's support is still in beta. It's recomendend to use Java 8. More information is available here
To install Nexflow all you need is to run the following command:
curl -s https://get.nextflow.io | bash
This will create the nextflow executable in the current directory. You then can add this to your $PATH environment variable with export PATH=$PATH:/path/to/current/dir or by adding this to the ~/.bashrc file (or equivalent).
More instructions are available here.
All components of DEN-IM are executed in docker containers, which means that you’ll need to have a container engine installed before using DEN-IM. This removed the burden of having to manually install all of the software which DEN-IM depends on.
The container engines available are the ones supported by Nextflow: - Docker, - Singularity, - Shifter (undocumented)
If you already have any one of these installed, you are good to go as the provided docker containers are compatible with all engines available. If not, you’ll need to install one. The installation instructions will depend on the chosen engine.
In an Ubuntu system, you can install Docker by following these instructions. These optional post installation steps are often necessary to get Docker to run. Alternatively, Singularity installation instructions are available here.
When executing a Nextflow pipeline, like DEN-IM, you'll need to set the profile according to what engine you have installed. With docker you'll need to provide the -profile docker option. With DEN-IM singularity is already set as the default engine so no parameter needs to be provided. The full list of supported profiles by DEN-IM is available here.
Upon DEN-IM's execution, the necessary containers will automatically be downloaded by Nextflow.
For a local installation of DEN-IM, you can clone this repository with git clone https://github.com/B-UMMI/DEN-IM.git, and all files will e cloned to your local machine.
The local installation of the DEN-IM workflow, including the docker containers with all the tools needed and the curated DENV database, requires 15 Gigabytes of free disk space.
Alternatively, you can run DEN-IM directly with nextflow with the command nextflow run B-UMMI/DEN-IM.
The minimum requirements to execute the workflow are at least 5 Gigabytes of memory and 4 CPUs, although 7 Gigabytes of memory is advised. The disk space required for execution depends greatly on the size of the input data, but for the datasets used in this article, DEN-IM generates approximately 20 Gb of data per Gb input data.
More information on how to execute DEN-IM in available in the How to Run DEN-IM page.